Q: So, some of the mails will get rejected/tickets will not be created right ?

A: That is my experience. Some times a really bad email (I find bounce messages in my organization) some times hang up and throw errors. Logging into the IMAP box and deleting the offending email always fixes it. [note this does not happen very often at all and I haven't really figured out the why yet.]

Means, is there anything to check in the missing mails, Ex : size of the mail, Attachment size etc .... if any limitation are there, please let me know so that i will keep an eye on the missing mails in detail.